GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Synechococcus elongatus PCC 7942

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__SynE:Synpcc7942_2495
          Length = 313

 Score =  141 bits (355), Expect = 2e-38
 Identities = 99/306 (32%), Positives = 166/306 (54%), Gaps = 25/306 (8%)

Query: 1   MDLSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTW---------- 50
           MD  Q + NG+A+G + AL A+G TL + IL + NFAHG   TL AYLT+          
Sbjct: 1   MDWLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFN 60

Query: 51  --WANTS---GINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALF 105
              AN +    +   L++ LG +    A  + E + ++P+R R+A     +I S+G+A+F
Sbjct: 61  GLLANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVF 120

Query: 106 LRNGILLIWGGNNQNYRVPI---VPAQDFMG-----IKFEYYRLLVIAMAIAAMVVLHLI 157
           + N I ++ G     +   I   +P+   +G     I+    ++++  +AIA   +L  +
Sbjct: 121 IVNLIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWL 180

Query: 158 LQRTKVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLK-PNM 216
           +  T+VG A++AVA++   A + GI+ +  +  T+ ++ VL  L G++ G   ++  P  
Sbjct: 181 INGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYF 240

Query: 217 GWFLILPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI 276
           G    L   + ++LGG+GN  G IAGG+++G+A E  VP   + Y+  VA  L+  +L I
Sbjct: 241 GIAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLA-EAWVPPQWSGYRDAVAFALLFAMLLI 299

Query: 277 RPQGLF 282
           RPQGLF
Sbjct: 300 RPQGLF 305


Lambda     K      H
   0.329    0.143    0.450 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 237
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 286
Length of database: 313
Length adjustment: 27
Effective length of query: 259
Effective length of database: 286
Effective search space:    74074
Effective search space used:    74074
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory